Probabilistic inference for nucleosome positioning with mnase-based or sonicated short-read data

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Zhang, Xuekui ^a   Robertson, Gordon ^b   Woo, Sangsoon ^c   Hoffman, Brad G ^a,d   Gottardo, Raphael ^c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c Fred Hutchinson Cancer Research Center   (United States)

^d BC CHILDREN S HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; HEPATOCYTE NUCLEAR FACTOR 3BETA; MICROCOCCAL NUCLEASE; TAMOXIFEN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR PDX 1; FOXA2 PROTEIN, MOUSE; HISTONE; HOMEODOMAIN PROTEIN; PANCREATIC AND DUODENAL HOMEOBOX 1 PROTEIN; TRANSACTIVATOR PROTEIN;

ACCURACY; ALGORITHM; ARTICLE; BAYES THEOREM; BINDING SITE; CELL INTERACTION; CELLULAR DISTRIBUTION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA ANALYSIS; DNA FLANKING REGION; DNA TEMPLATE; GENE EXPRESSION REGULATION; GENE LOCUS; GENETIC ASSOCIATION; HISTONE MODIFICATION; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PREDICTION; PROBABILISTIC INFERENCE FOR NUCLEOSOME POSITIONING MODEL; REFERENCE DATABASE; SENSITIVITY AND SPECIFICITY; STATISTICAL DISTRIBUTION; STATISTICAL MODEL; ANIMAL; AREA UNDER THE CURVE; BIOLOGY; CHEMISTRY; GENE EXPRESSION PROFILING; HUMAN; METABOLISM; METHODOLOGY; MOUSE; NUCLEOSOME; PANCREAS ISLET; PROBABILITY; REPRODUCIBILITY;

ALGORITHMS; ANIMALS; AREA UNDER CURVE; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HEPATOCYTE NUCLEAR FACTOR 3-BETA; HISTONES; HOMEODOMAIN PROTEINS; HUMANS; ISLETS OF LANGERHANS; MICE; MICROCOCCAL NUCLEASE; MODELS, STATISTICAL; NUCLEOSOMES; PROBABILITY; REPRODUCIBILITY OF RESULTS; TAMOXIFEN; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 84863290812     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032095     Document Type: Article

References (35)

1. Jiang C, Pugh B, (2009) A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biology 10: R109.
2. Radman-Livaja M, Rando OJ, (2010) Nucleosome positioning: how is it established, and why does it matter? Developmental biology 339: 258-266.
3. Conerly ML, Teves SS, Diolaiti D, Ulrich M, Eisenman RN, et al. (2010) Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. Genome Research 20: 1383-1390.
4. Elsaesser SJ, Goldberg AD, Allis CD, (2010) New functions for an old variant: no substitute for histone H3.3. Current opinion in genetics & development 20: 110-117.
5. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, et al. (2010) Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140: 678-691.
6. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reect global cell-type-specific gene expression. Nature 459: 108-112.
7. Zhang Z, Pugh BF, (2011) High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144: 175-186.
8. Clark DJ, (2010) Nucleosome positioning, nucleosome spacing and the nucleosome code. Journal of biomolecular structure & dynamics 27: 781-793.
9. Roy S, Ernst J, Kharchenko PV, Kheradpour P, et al. modENCODE Consortium (2010) Identification of functional elements and regulatory circuits by drosophila modencode. Science 330: 1787-97.
10. Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-25.
11. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nature biotechnology 28: 1045-1048.
12. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
13. Barski A, Cuddapah S, Cui K, Roh T, Schones D, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
14. Zhang Y, Shin H, Song JS, Lei Y, Liu XS, (2008) Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC genomics 9: 537.
15. Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N, (2010) High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Research 20: 90-100.
16. Kuan PF, Huebert D, Gasch A, Keles S, (2009) A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions. Statistical Applications in Genetics and Molecular Biology 8: Article29.
17. He HH, Meyer CA, Shin H, Bailey ST, Wei G, et al. (2010) Nucleosome dynamics define transcriptional enhancers. Nature Genetics 42: 343-347.
18. Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, et al. (2010) PICS: Probabilistic Inference for ChIP-seq. Biometrics 67: 151-163.
19. Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, et al. (2010) Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. Genome Research 20: 1037-1051.
20. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, et al. (2010) Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Molecular Cell 38: 576-589.
21. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
22. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature biotechnology 27: 66-75.
23. Besag J, Kooperberg C, (1995) On conditional and intrinsic autoregressions. Biometrika 82: 733-746.
24. Lo K, Gottardo R, (2007) Flexible empirical bayes models for differential gene expression. Bioinformatics 23: 328-35.
25. Kendziorski CM, Newton MA, Lan H, Gould MN, (2003) On parametric empirical bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med 22: 3899-914.
26. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, et al. (2008) Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Research 18: 1906-1917.
27. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.
28. Cirillo LA, Zaret KS, (2007) Specific interactions of the wing domains of FOXA1 transcription factor with DNA. Journal of Molecular Biology 366: 720-724.
29. Kim H, Toyofuku Y, Lynn FC, Chak E, Uchida T, et al. (2010) Serotonin regulates pancreatic beta cell mass during pregnancy. Nature Medicine 16: 804-808.
30. Munzel U, (2001) A unified approach to simultaneous rank test procedures in the unbalanced oneway layout. Biometrical Journal 43: 553-569.
31. Ong MS, Richmond TJ, Davey CA, (2007) DNA stretching and extreme kinking in the nucleosome core. Journal of Molecular Biology 368: 1067-1074.
32. Li G, Widom J, (2004) Nucleosomes facilitate their own invasion. Nature Structural & Molecular Biology 11: 763-769.
33. Edayathumangalam RS, Weyermann P, Gottesfeld JM, Dervan PB, Luger K, (2004) Molecular recognition of the nucleosomal "supergroove". Proceedings of the National Academy of Sciences of the United States of America 101: 6864-6869.
34. Longo A, Guanga GP, Rose RB, (2007) Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain. Biochemistry 46: 2948-2957.
35. Tong E, Guo J, Xu S, Mak K, Chung S, et al. (2009) Inducible nucleosome depletion at OREBP-binding-sites by hypertonic stress. PLoS One 4: e8435.